Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::idealize::IdealizeMover Class Reference

Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points. More...

#include <IdealizeMover.hh>

Inheritance diagram for protocols::idealize::IdealizeMover:
Inheritance graph
[legend]

Public Types

typedef core::Real Real
 
typedef core::pose::Pose Pose
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 IdealizeMover ()
 
moves::MoverOP clone () const override
 clone has to be overridden only if clone invocation is expected. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
IdealizeMoveratom_pair_constraint_weight (core::Real const setting)
 
IdealizeMovercoordinate_constraint_weight (core::Real const setting)
 
IdealizeMoverfast (bool const setting)
 
IdealizeMoverchainbreaks (bool const setting)
 
IdealizeMovercis_omega (bool const setting)
 
IdealizeMoverreport_CA_rmsd (bool const setting)
 
void apply (Pose &pose) override
 Main Method. More...
 
void set_pos_list (utility::vector1< core::Size > pos_list)
 Sets the list of residue positions to idealize. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
core::select::residue_selector::ResidueSelectorCOP ignore_residues_in_csts () const
 
void ignore_residues_in_csts (core::select::residue_selector::ResidueSelectorCOP const &i)
 
void impose_constraints (bool const i)
 
bool impose_constraints () const
 
bool constraints_only () const
 
void constraints_only (bool const c)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
virtual void test_move (Pose &pose)
 : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
 
virtual bool reinitialize_for_each_job () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
virtual bool reinitialize_for_new_input () const
 Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
 
MoverStatus get_last_move_status () const
 end parser interface, start Job Distributor interface///////////// More...
 
void reset_status ()
 resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
 
virtual core::pose::PoseOP get_additional_output ()
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
std::string get_current_tag () const
 A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void clear_info ()
 Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
 
virtual Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Private Member Functions

void setup_idealize_constraints (Pose &pose)
 Add the idealize constraints to the pose's constraint set. More...
 

Private Attributes

utility::vector1< core::Sizepos_list_
 
Real atom_pair_constraint_weight_
 
Real coordinate_constraint_weight_
 
core::select::residue_selector::ResidueSelectorCOP ignore_residues_in_csts_
 
bool cis_omega_
 
bool fast_
 
bool chainbreaks_
 
bool report_CA_rmsd_
 
bool impose_constraints_
 
bool constraints_only_
 

Additional Inherited Members

- Protected Member Functions inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Detailed Description

Mover class for transforming a Pose to ideal bonds of the given Pose. The idea is that this Mover stochastically picks a move-able position, forces that position into ideal geometry, and tries to use minimization to bring the coordinates back to very near their starting points.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::idealize::IdealizeMover::IdealizeMover ( )
inline

Member Function Documentation

void protocols::idealize::IdealizeMover::apply ( Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::chemical::aa_vrt, core::scoring::all_atom_rmsd(), core::pose::Pose::append_residue_by_jump(), core::scoring::atom_pair_constraint, protocols::idealize::basic_idealize(), core::scoring::CA_rmsd(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::conformation::ResidueFactory::create_residue(), core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dst, core::pose::Pose::fold_tree(), core::pose::Pose::is_fullatom(), core::pose::symmetry::is_symmetric(), core::scoring::pro_close, core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::idealize::TR(), and core::pose::virtual_type_for_pose().

Referenced by protocols::frag_picker::nonlocal::NonlocalFrags::apply(), protocols::abinitio::KinematicAbinitio::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxApplication::close_loops(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::abinitio::AbrelaxApplication::fold(), protocols::match::downstream::LigandConformerBuilder::initialize_conformers(), protocols::cluster::ClusterBase::print_cluster_PDBs(), protocols::cluster::ClusterBase::print_clusters_silentfile(), protocols::struct_fragment::StructFragmentMover::steal_fragments(), and protocols::jobdist::universal_main().

IdealizeMover& protocols::idealize::IdealizeMover::atom_pair_constraint_weight ( core::Real const  setting)
inline
IdealizeMover& protocols::idealize::IdealizeMover::chainbreaks ( bool const  setting)
inline
IdealizeMover& protocols::idealize::IdealizeMover::cis_omega ( bool const  setting)
inline

References cis_omega_.

moves::MoverOP protocols::idealize::IdealizeMover::clone ( ) const
inlineoverridevirtual

clone has to be overridden only if clone invocation is expected.

Reimplemented from protocols::moves::Mover.

bool protocols::idealize::IdealizeMover::constraints_only ( ) const
inline

References constraints_only_.

void protocols::idealize::IdealizeMover::constraints_only ( bool const  c)
inline
IdealizeMover& protocols::idealize::IdealizeMover::coordinate_constraint_weight ( core::Real const  setting)
inline
IdealizeMover& protocols::idealize::IdealizeMover::fast ( bool const  setting)
inline
moves::MoverOP protocols::idealize::IdealizeMover::fresh_instance ( ) const
inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::idealize::IdealizeMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

core::select::residue_selector::ResidueSelectorCOP protocols::idealize::IdealizeMover::ignore_residues_in_csts ( ) const
void protocols::idealize::IdealizeMover::ignore_residues_in_csts ( core::select::residue_selector::ResidueSelectorCOP const &  i)
void protocols::idealize::IdealizeMover::impose_constraints ( bool const  i)
inline

References impose_constraints_.

bool protocols::idealize::IdealizeMover::impose_constraints ( ) const
inline

References impose_constraints_.

std::string protocols::idealize::IdealizeMover::mover_name ( )
static
void protocols::idealize::IdealizeMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::pose::get_resnum_selector(), and protocols::idealize::TR().

void protocols::idealize::IdealizeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
IdealizeMover& protocols::idealize::IdealizeMover::report_CA_rmsd ( bool const  setting)
inline
void protocols::idealize::IdealizeMover::set_pos_list ( utility::vector1< core::Size pos_list)
inline

Sets the list of residue positions to idealize.

References pos_list_.

void protocols::idealize::IdealizeMover::setup_idealize_constraints ( Pose pose)
private

Member Data Documentation

Real protocols::idealize::IdealizeMover::atom_pair_constraint_weight_
private
bool protocols::idealize::IdealizeMover::chainbreaks_
private

Referenced by chainbreaks().

bool protocols::idealize::IdealizeMover::cis_omega_
private

Referenced by cis_omega().

bool protocols::idealize::IdealizeMover::constraints_only_
private

Referenced by constraints_only().

Real protocols::idealize::IdealizeMover::coordinate_constraint_weight_
private
bool protocols::idealize::IdealizeMover::fast_
private

Referenced by fast().

core::select::residue_selector::ResidueSelectorCOP protocols::idealize::IdealizeMover::ignore_residues_in_csts_
private
bool protocols::idealize::IdealizeMover::impose_constraints_
private

Referenced by impose_constraints().

utility::vector1< core::Size > protocols::idealize::IdealizeMover::pos_list_
private

Referenced by set_pos_list().

bool protocols::idealize::IdealizeMover::report_CA_rmsd_
private

Referenced by report_CA_rmsd().


The documentation for this class was generated from the following files: